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Pérez-Pertejo Y, García-Estrada C, Martínez-Valladares M, Murugesan S, Reguera RM, Balaña-Fouce R. Polyamine Metabolism for Drug Intervention in Trypanosomatids. Pathogens 2024; 13:79. [PMID: 38251386 PMCID: PMC10820115 DOI: 10.3390/pathogens13010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Neglected tropical diseases transmitted by trypanosomatids include three major human scourges that globally affect the world's poorest people: African trypanosomiasis or sleeping sickness, American trypanosomiasis or Chagas disease and different types of leishmaniasis. Different metabolic pathways have been targeted to find antitrypanosomatid drugs, including polyamine metabolism. Since their discovery, the naturally occurring polyamines, putrescine, spermidine and spermine, have been considered important metabolites involved in cell growth. With a complex metabolism involving biosynthesis, catabolism and interconversion, the synthesis of putrescine and spermidine was targeted by thousands of compounds in an effort to produce cell growth blockade in tumor and infectious processes with limited success. However, the discovery of eflornithine (DFMO) as a curative drug against sleeping sickness encouraged researchers to develop new molecules against these diseases. Polyamine synthesis inhibitors have also provided insight into the peculiarities of this pathway between the host and the parasite, and also among different trypanosomatid species, thus allowing the search for new specific chemical entities aimed to treat these diseases and leading to the investigation of target-based scaffolds. The main molecular targets include the enzymes involved in polyamine biosynthesis (ornithine decarboxylase, S-adenosylmethionine decarboxylase and spermidine synthase), enzymes participating in their uptake from the environment, and the enzymes involved in the redox balance of the parasite. In this review, we summarize the research behind polyamine-based treatments, the current trends, and the main challenges in this field.
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Affiliation(s)
- Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Campus de Vegazana s/n, Universidad de León, 24071 León, Spain; (Y.P.-P.); (C.G.-E.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Campus de Vegazana s/n, Universidad de León, 24071 León, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Campus de Vegazana s/n, Universidad de León, 24071 León, Spain; (Y.P.-P.); (C.G.-E.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Campus de Vegazana s/n, Universidad de León, 24071 León, Spain
| | | | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Pilani 333031, India;
| | - Rosa M. Reguera
- Departamento de Ciencias Biomédicas, Campus de Vegazana s/n, Universidad de León, 24071 León, Spain; (Y.P.-P.); (C.G.-E.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Campus de Vegazana s/n, Universidad de León, 24071 León, Spain
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Campus de Vegazana s/n, Universidad de León, 24071 León, Spain; (Y.P.-P.); (C.G.-E.); (R.M.R.)
- Instituto de Biomedicina (IBIOMED), Campus de Vegazana s/n, Universidad de León, 24071 León, Spain
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2
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Jamabo M, Mahlalela M, Edkins AL, Boshoff A. Tackling Sleeping Sickness: Current and Promising Therapeutics and Treatment Strategies. Int J Mol Sci 2023; 24:12529. [PMID: 37569903 PMCID: PMC10420020 DOI: 10.3390/ijms241512529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Human African trypanosomiasis is a neglected tropical disease caused by the extracellular protozoan parasite Trypanosoma brucei, and targeted for eradication by 2030. The COVID-19 pandemic contributed to the lengthening of the proposed time frame for eliminating human African trypanosomiasis as control programs were interrupted. Armed with extensive antigenic variation and the depletion of the B cell population during an infectious cycle, attempts to develop a vaccine have remained unachievable. With the absence of a vaccine, control of the disease has relied heavily on intensive screening measures and the use of drugs. The chemotherapeutics previously available for disease management were plagued by issues such as toxicity, resistance, and difficulty in administration. The approval of the latest and first oral drug, fexinidazole, is a major chemotherapeutic achievement for the treatment of human African trypanosomiasis in the past few decades. Timely and accurate diagnosis is essential for effective treatment, while poor compliance and resistance remain outstanding challenges. Drug discovery is on-going, and herein we review the recent advances in anti-trypanosomal drug discovery, including novel potential drug targets. The numerous challenges associated with disease eradication will also be addressed.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
| | - Maduma Mahlalela
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
| | - Adrienne L. Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Centre (BioBRU), Rhodes University, Makhanda 6139, South Africa;
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, South Africa; (M.J.); (M.M.)
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3
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Pardali V, Giannakopoulou E, Balourdas DI, Myrianthopoulos V, Taylor MC, Šekutor M, Mlinarić-Majerski K, Kelly JM, Zoidis G. Lipophilic Guanylhydrazone Analogues as Promising Trypanocidal Agents: An Extended SAR Study. Curr Pharm Des 2020; 26:838-866. [DOI: 10.2174/1381612826666200210150127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022]
Abstract
In this report, we extend the SAR analysis of a number of lipophilic guanylhydrazone analogues with
respect to in vitro growth inhibition of Trypanosoma brucei and Trypanosoma cruzi. Sleeping sickness and Chagas
disease, caused by the tropical parasites T. brucei and T. cruzi, constitute a significant socioeconomic burden
in low-income countries of sub-Saharan Africa and Latin America, respectively. Drug development is underfunded.
Moreover, current treatments are outdated and difficult to administer, while drug resistance is an emerging
concern. The synthesis of adamantane-based compounds that have potential as antitrypanosomal agents is
extensively reviewed. The critical role of the adamantane ring was further investigated by synthesizing and testing
a number of novel lipophilic guanylhydrazones. The introduction of hydrophobic bulky substituents onto the
adamantane ring generated the most active analogues, illustrating the synergistic effect of the lipophilic character
of the C1 side chain and guanylhydrazone moiety on trypanocidal activity. The n-decyl C1-substituted compound
G8 proved to be the most potent adamantane derivative against T. brucei with activity in the nanomolar range
(EC50=90 nM). Molecular simulations were also performed to better understand the structure-activity relationships
between the studied guanylhydrazone analogues and their potential enzyme target.
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Affiliation(s)
- Vasiliki Pardali
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Erofili Giannakopoulou
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Dimitrios-Ilias Balourdas
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Vassilios Myrianthopoulos
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Martin C. Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruder Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - Kata Mlinarić-Majerski
- Department of Organic Chemistry and Biochemistry, Ruder Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
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Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Emerging concepts in pseudoenzyme classification, evolution, and signaling. Sci Signal 2019; 12:eaat9797. [PMID: 31409758 DOI: 10.1126/scisignal.aat9797] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 21st century is witnessing an explosive surge in our understanding of pseudoenzyme-driven regulatory mechanisms in biology. Pseudoenzymes are proteins that have sequence homology with enzyme families but that are proven or predicted to lack enzyme activity due to mutations in otherwise conserved catalytic amino acids. The best-studied pseudoenzymes are pseudokinases, although examples from other families are emerging at a rapid rate as experimental approaches catch up with an avalanche of freely available informatics data. Kingdom-wide analysis in prokaryotes, archaea and eukaryotes reveals that between 5 and 10% of proteins that make up enzyme families are pseudoenzymes, with notable expansions and contractions seemingly associated with specific signaling niches. Pseudoenzymes can allosterically activate canonical enzymes, act as scaffolds to control assembly of signaling complexes and their localization, serve as molecular switches, or regulate signaling networks through substrate or enzyme sequestration. Molecular analysis of pseudoenzymes is rapidly advancing knowledge of how they perform noncatalytic functions and is enabling the discovery of unexpected, and previously unappreciated, functions of their intensively studied enzyme counterparts. Notably, upon further examination, some pseudoenzymes have previously unknown enzymatic activities that could not have been predicted a priori. Pseudoenzymes can be targeted and manipulated by small molecules and therefore represent new therapeutic targets (or anti-targets, where intervention should be avoided) in various diseases. In this review, which brings together broad bioinformatics and cell signaling approaches in the field, we highlight a selection of findings relevant to a contemporary understanding of pseudoenzyme-based biology.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sayoni Das
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Natalie Dawson
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christine Orengo
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Building, Room 8.109, University of Leeds, Leeds LS2 9JT, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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5
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Patel MM, Volkov OA, Leija C, Lemoff A, Phillips MA. A dual regulatory circuit consisting of S-adenosylmethionine decarboxylase protein and its reaction product controls expression of the paralogous activator prozyme in Trypanosoma brucei. PLoS Pathog 2018; 14:e1007404. [PMID: 30365568 PMCID: PMC6221367 DOI: 10.1371/journal.ppat.1007404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/07/2018] [Accepted: 10/12/2018] [Indexed: 01/12/2023] Open
Abstract
Polyamines are essential for cell growth of eukaryotes including the etiologic agent of human African trypanosomiasis (HAT), Trypanosoma brucei. In trypanosomatids, a key enzyme in the polyamine biosynthetic pathway, S-adenosylmethionine decarboxylase (TbAdoMetDC) heterodimerizes with a unique catalytically-dead paralog called prozyme to form the active enzyme complex. In higher eukaryotes, polyamine metabolism is subject to tight feedback regulation by spermidine-dependent mechanisms that are absent in trypanosomatids. Instead, in T. brucei an alternative regulatory strategy based on TbAdoMetDC prozyme has evolved. We previously demonstrated that prozyme protein levels increase in response to loss of TbAdoMetDC activity. Herein, we show that prozyme levels are under translational control by monitoring incorporation of deuterated leucine into nascent prozyme protein. We furthermore identify pathway factors that regulate prozyme mRNA translation. We find evidence for a regulatory feedback mechanism in which TbAdoMetDC protein and decarboxylated AdoMet (dcAdoMet) act as suppressors of prozyme translation. In TbAdoMetDC null cells expressing the human AdoMetDC enzyme, prozyme levels are constitutively upregulated. Wild-type prozyme levels are restored by complementation with either TbAdoMetDC or an active site mutant, suggesting that TbAdoMetDC possesses an enzyme activity-independent function that inhibits prozyme translation. Depletion of dcAdoMet pools by three independent strategies: inhibition/knockdown of TbAdoMetDC, knockdown of AdoMet synthase, or methionine starvation, each cause prozyme upregulation, providing independent evidence that dcAdoMet functions as a metabolic signal for regulation of the polyamine pathway in T. brucei. These findings highlight a potential regulatory paradigm employing enzymes and pseudoenzymes that may have broad implications in biology. Trypanosoma brucei is a single-celled eukaryotic pathogen and the causative agent of human African trypanosomiasis (HAT). Polyamines are organic polycations that are essential for growth in T. brucei to facilitate protein translation and to maintain redox homeostasis. The pathway is the target of eflornithine, a current frontline therapy for treatment of HAT. Polyamine biosynthetic enzymes are regulated at multiple levels in mammals (e.g. transcription, translation and protein turnover), but in contrast, T. brucei lacks these mechanisms. Instead in T. brucei a central enzyme in polyamine metabolism called AdoMetDC must form a complex with a sister protein (termed a pseudoenzyme) to be active. Herein, we show that cellular levels of this sister protein we call prozyme are in turn feedback regulated by both AdoMetDC and by its reaction product in response to cell treatments that reduce pathway output. This regulatory paradigm highlights how pseudoenzymes can evolve to play an important role in metabolic pathway regulation and in organismal fitness.
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Affiliation(s)
- Manish M. Patel
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Oleg A. Volkov
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Christopher Leija
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
- * E-mail:
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6
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Synthesis and evaluation of analogs of 5'-(((Z)-4-amino-2-butenyl)methylamino)-5'-deoxyadenosine (MDL 73811, or AbeAdo) - An inhibitor of S-adenosylmethionine decarboxylase with antitrypanosomal activity. Bioorg Med Chem 2017; 25:5433-5440. [PMID: 28807574 DOI: 10.1016/j.bmc.2017.07.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/31/2017] [Indexed: 01/18/2023]
Abstract
We describe our efforts to improve the pharmacokinetic properties of a mechanism-based suicide inhibitor of the polyamine biosynthetic enzyme S-adenosylmethionine decarboxylase (AdoMetDC), essential for the survival of the eukaryotic parasite Trypanosoma brucei responsible for Human African Trypanosomiasis (HAT). The lead compound, 5'-(((Z)-4-amino-2-butenyl)methylamino)-5'-deoxyadenosine (1, also known as MDL 73811, or AbeAdo), has curative efficacy at a low dosage in a hemolymphatic model of HAT but displayed no demonstrable effect in a mouse model of the CNS stage of HAT due to poor blood-brain barrier permeation. Therefore, we prepared and evaluated an extensive set of analogs with modifications in the aminobutenyl side chain, the 5'-amine, the ribose, and the purine fragments. Although we gained valuable structure-activity insights from this comprehensive dataset, we did not gain traction on improving the prospects for CNS penetration while retaining the potent antiparasitic activity and metabolic stability of the lead compound 1.
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7
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Volkov OA, Cosner CC, Brockway AJ, Kramer M, Booker M, Zhong S, Ketcherside A, Wei S, Longgood J, McCoy M, Richardson TE, Wring SA, Peel M, Klinger JD, Posner BA, De Brabander JK, Phillips MA. Identification of Trypanosoma brucei AdoMetDC Inhibitors Using a High-Throughput Mass Spectrometry-Based Assay. ACS Infect Dis 2017; 3:512-526. [PMID: 28350440 DOI: 10.1021/acsinfecdis.7b00022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human African trypanosomiasis (HAT) is a fatal infectious disease caused by the eukaryotic pathogen Trypanosoma brucei (Tb). Available treatments are difficult to administer and have significant safety issues. S-Adenosylmethionine decarboxylase (AdoMetDC) is an essential enzyme in the parasite polyamine biosynthetic pathway. Previous attempts to develop TbAdoMetDC inhibitors into anti-HAT therapies failed due to poor brain exposure. Here, we describe a large screening campaign of two small-molecule libraries (∼400,000 compounds) employing a new high-throughput (∼7 s per sample) mass spectrometry-based assay for AdoMetDC activity. As a result of primary screening, followed by hit confirmation and validation, we identified 13 new classes of reversible TbAdoMetDC inhibitors with low-micromolar potency (IC50) against both TbAdoMetDC and T. brucei parasite cells. The majority of these compounds were >10-fold selective against the human enzyme. Importantly, compounds from four classes demonstrated high propensity to cross the blood-brain barrier in a cell monolayer assay. Biochemical analysis demonstrated that compounds from eight classes inhibited intracellular TbAdoMetDC in the parasite, although evidence for a secondary off-target component was also present. The discovery of several new TbAdoMetDC inhibitor chemotypes provides new hits for lead optimization programs aimed to deliver a novel treatment for HAT.
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Affiliation(s)
| | | | | | - Martin Kramer
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
| | - Michael Booker
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
| | | | | | | | | | | | - Thomas E. Richardson
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Stephen A. Wring
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Michael Peel
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Jeffrey D. Klinger
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
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8
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Murphy JM, Farhan H, Eyers PA. Bio-Zombie: the rise of pseudoenzymes in biology. Biochem Soc Trans 2017; 45:537-544. [PMID: 28408493 DOI: 10.1042/bst20160400] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/17/2022]
Abstract
Pseudoenzymes are catalytically dead counterparts of enzymes. Despite their first description some 50 years ago, the importance and functional diversity of these 'fit-for-purpose' polypeptides is only now being appreciated. Pseudoenzymes have been identified throughout all the kingdoms of life and, owing to predicted deficits in enzyme activity due to the absence of catalytic residues, have been variously referred to as pseudoenzymes, non-enzymes, dead enzymes, prozymes or 'zombie' proteins. An important goal of the recent Biochemical Society Pseudoenzymes-focused meeting was to explore the functional and evolutionary diversity of pseudoenzymes and to begin to evaluate their functions in biology, including cell signalling and metabolism. Here, we summarise the impressive breadth of enzyme classes that are known to have pseudoenzyme counterparts and present examples of known cellular functions. We predict that the next decades will represent golden years for the analysis of pseudoenzymes.
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Affiliation(s)
- James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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9
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Kafková L, Debler EW, Fisk JC, Jain K, Clarke SG, Read LK. The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex. J Biol Chem 2016; 292:2089-2100. [PMID: 27998975 DOI: 10.1074/jbc.m116.757112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/14/2016] [Indexed: 11/06/2022] Open
Abstract
Prozymes are catalytically inactive enzyme paralogs that dramatically stimulate the function of weakly active enzymes through complex formation. The two prozymes described to date reside in the polyamine biosynthesis pathway of the human parasite Trypanosoma brucei, an early branching eukaryote that lacks transcriptional regulation and regulates its proteome through posttranscriptional and posttranslational means. Arginine methylation is a common posttranslational modification in eukaryotes catalyzed by protein arginine methyltransferases (PRMTs) that are typically thought to function as homodimers. We demonstrate that a major T. brucei PRMT, TbPRMT1, functions as a heterotetrameric enzyme-prozyme pair. The inactive PRMT paralog, TbPRMT1PRO, is essential for catalytic activity of the TbPRMT1ENZ subunit. Mutational analysis definitively demonstrates that TbPRMT1ENZ is the cofactor-binding subunit and carries all catalytic activity of the complex. Our results are the first demonstration of an obligate heteromeric PRMT, and they suggest that enzyme-prozyme organization is expanded in trypanosomes as a posttranslational means of enzyme regulation.
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Affiliation(s)
- Lucie Kafková
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Erik W Debler
- the Laboratory of Cell Biology, The Rockefeller University, New York, New York 10065, and
| | - John C Fisk
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214
| | - Kanishk Jain
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- the Department of Chemistry and Biochemistry and The Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Laurie K Read
- From the Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, and Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214,
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10
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. eLife 2016; 5. [PMID: 27977001 PMCID: PMC5201418 DOI: 10.7554/elife.20198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/11/2016] [Indexed: 02/06/2023] Open
Abstract
Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved. DOI:http://dx.doi.org/10.7554/eLife.20198.001
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Affiliation(s)
- Oleg A Volkov
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carson Ariagno
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shihua Zhong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute,University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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11
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Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PLoS Pathog 2016; 12:e1006010. [PMID: 27820863 PMCID: PMC5098729 DOI: 10.1371/journal.ppat.1006010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/18/2016] [Indexed: 01/17/2023] Open
Abstract
The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK) catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD), which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA), which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5'-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5'-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug.
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Affiliation(s)
- Christopher Leija
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Filipa Rijo-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Lisa N. Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zeping Hu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
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Novel protein-protein interaction between spermidine synthase and S-adenosylmethionine decarboxylase from Leishmania donovani. Biochem Biophys Res Commun 2014; 456:637-42. [PMID: 25511700 DOI: 10.1016/j.bbrc.2014.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 12/03/2014] [Indexed: 11/23/2022]
Abstract
Polyamine biosynthesis pathway has long been considered an essential drug target for trypanosomatids including Leishmania. S-adenosylmethionine decarboxylase (AdoMetDc) and spermidine synthase (SpdSyn) are enzymes of this pathway that catalyze successive steps, with the product of the former, decarboxylated S-adenosylmethionine (dcSAM), acting as an aminopropyl donor for the latter enzyme. Here we have explored the possibility of and identified the protein-protein interaction between SpdSyn and AdoMetDc. The protein-protein interaction has been identified using GST pull down assay. Isothermal titration calorimetry reveals that the interaction is thermodynamically favorable. Fluorescence spectroscopy studies also confirms the interaction, with SpdSyn exhibiting a change in tertiary structure with increasing concentrations of AdoMetDc. Size exclusion chromatography suggests the presence of the complex as a hetero-oligomer. Taken together, these results suggest that the enzymes indeed form a heteromer. Computational analyses suggest that this complex differs significantly from the corresponding human complex, implying that this complex could be a better therapeutic target than the individual enzymes.
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13
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Genetic validation of Trypanosoma brucei glutathione synthetase as an essential enzyme. EUKARYOTIC CELL 2014; 13:614-24. [PMID: 24610661 DOI: 10.1128/ec.00015-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human African trypanosomiasis (HAT) is a debilitating and fatal vector-borne disease. Polyamine biosynthesis is the target of one of the key drugs (eflornithine) used for the treatment of late-stage disease, suggesting that the pathway might be exploited for the identification of additional drug targets. The polyamine spermidine is required in trypanosomatid parasites for formation of a unique redox cofactor termed trypanothione, which is formed from the conjugation of glutathione to spermidine. Here we characterize recombinant Trypanosoma brucei glutathione synthetase (TbGS) and show that depletion of TbGS in blood-form parasites using a regulated knockout strategy leads to loss of trypanothione and to cell death as quantified by fluorescence-activated cell sorter (FACS) analysis. These data suggest that >97% depletion of TbGS is required before trypanothione is depleted and cell growth arrest is observed. Exogenous glutathione was able to partially compensate for the loss of TbGS, suggesting that parasites are able to transport intact glutathione. Finally, reduced expression of TbGS leads to increased levels of upstream glutathione biosynthetic enzymes and decreased expression of polyamine biosynthetic enzymes, providing evidence that the cells cross regulate the two branches of the trypanothione biosynthetic pathway to maintain spermidine and trypanothione homeostasis.
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14
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Target-based drug discovery for human African trypanosomiasis: selection of molecular target and chemical matter. Parasitology 2013; 141:28-36. [PMID: 23931634 PMCID: PMC3884840 DOI: 10.1017/s0031182013001017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Target-based approaches for human African trypanosomiasis (HAT) and related parasites can be a valuable route for drug discovery for these diseases. However, care needs to be taken in selection of both the actual drug target and the chemical matter that is developed. In this article, potential criteria to aid target selection are described. Then the physiochemical properties of typical oral drugs are discussed and compared to those of known anti-parasitics.
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15
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Xiao Y, Nguyen S, Kim SH, Volkov OA, Tu BP, Phillips MA. Product feedback regulation implicated in translational control of the Trypanosoma brucei S-adenosylmethionine decarboxylase regulatory subunit prozyme. Mol Microbiol 2013; 88:846-61. [PMID: 23634831 DOI: 10.1111/mmi.12226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 12/12/2022]
Abstract
Human African sleeping sickness (HAT) is caused by the parasitic protozoan Trypanosoma brucei. Polyamine biosynthesis is an important drug target in the treatment of HAT. Previously we showed that trypanosomatid S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme for biosynthesis of the polyamine spermidine, is activated by heterodimer formation with an inactive paralogue termed prozyme. Furthermore, prozyme protein levels were regulated in response to reduced AdoMetDC activity. Herein we show that T. brucei encodes three prozyme transcripts. The 3'UTRs of these transcripts were mapped and chloramphenicol acetyltransferase (CAT) reporter constructs were used to identify a 1.2 kb region that contained a 3'UTR prozyme regulatory element sufficient to upregulate CAT protein levels (but not RNA) upon AdoMetDC inhibition, supporting the hypothesis that prozyme expression is regulated translationally. To gain insight into trans-acting factors, genetic rescue of AdoMetDC RNAi knock-down lines with human AdoMetDC was performed leading to rescue of the cell growth block, and restoration of prozyme protein to wild-type levels. Metabolite analysis showed that prozyme protein levels were inversely proportional to intracellular levels of decarboxylated AdoMet (dcAdoMet). These data suggest that prozyme translation may be regulated by dcAdoMet, a metabolite not previously identified to play a regulatory role.
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Affiliation(s)
- Yanjing Xiao
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
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